Collective movements are ubiquitous in biological systems, occurring at all scales; from the sub-organismal movements of groups of cells, to the far-ranging movements of bird flocks and herds of large herbivores. Movement patterns at these vastly different scales often exhibit surprisingly similar patterns, suggesting that mathematically similar mechanisms may drive collective movements across many systems. The aims of this study were three-fold. First, to develop mechanistic movement models capable of producing the observed wealth of spatial patterns. Second, to tailor statistical inference approaches to these models that are capable of identifying drivers of collective movement that could be applied to a wide range of study systems. Third, to validate the approaches by fitting the mechanistic models to data from diverse biological systems. These study systems included two small-scale in vitro cellular systems, involving movement of groups of human melanoma cells and Dictyostelium discoideum (slime mould) cells, and a third much larger-scale system, involving wildebeest in the Serengeti ecosystem. I developed a series of mechanistic movement models, based on advection-diffusion partial differential equations and integro-differential equations, that describe changes in the spatio-temporal distribution of the study population as a consequence of various movement drivers, including environmental gradients, environmental depletion, social behaviour, and spatial and temporal heterogeneity in the response of the individuals to these drivers. I also developed a number of approaches to statistical inference (comprising both parameter estimation and model comparison) for these models that ranged from frequentist, to pseudo-Bayesian, to fully Bayesian. These inference approaches also varied in whether they required numerical solutions of the models, or whether the need for numerical solutions was bypassed by using gradient matching methods. The inference methods were specifically designed to be effective in the face of the many difficulties presented by advection-diffusion models, particularly high computational costs and instabilities in numerical model solutions, which have previously prevented these models from being fitted to data. It was also necessary for these inference methods to be able to cope with data of different qualities; the cellular data provided accurate information on the locations of all individuals through time, while the wildebeest data consisted of coarse ordinal abundance categories on a spatial grid at monthly intervals. By applying the developed models and inference methods to data from each study system, I drew a number of conclusions about the mechanisms driving movement in these systems. In all three systems, for example, there was evidence of a saturating response to an environmental gradient in a resource or chemical attractant that the individuals could deplete locally. I also found evidence of temporal dependence in the movement parameters for all systems. This indicates that the simplifying assumption that behaviour is constant, which has been made by many previous studies that have modelled movement, is unlikely to be justified. Differences between the systems were also demonstrated, such as overcrowding affecting the movements of melanoma and wildebeest, but not Dictyostelium, and wildebeest having a much greater range of perception than cells, and thus being able to respond to environmental conditions tens of kilometres away. The toolbox of methods developed in this thesis could be applied to increase understanding of the mechanisms underlying collective movement in a wide range of systems. In their current form, these methods are capable of producing very close matches between models and data for our simple cell systems, and also produce a relatively good model fit in the more complex wildebeest system, where there is, however, still some room for improvement. While more work is required to make the models generalisable to all taxa, particularly through the addition of memory-driven movement, inter-individual differences in behaviour, and more complex social dynamics, the advection-diffusion modelling framework is flexible enough for these additional behaviours to be incorporated in the future. A greater understanding of what drives collective movements in different systems could allow management of these movements to prevent the collapse of important migrations, control pest species, or prevent the spread of cancer.

The leishmaniases are neglected tropical diseases with an urgent need for effective drugs. Better understanding of the metabolism of the causative parasites will hopefully lead to development of new compounds targeted at critical points of the parasite’s biochemical pathways. In my work I focused on the pentose phosphate pathway of Leishmania, specifically on transketolase, sugar utilisation, and comparison between insect and mammalian infective stages of the parasites. The pentose phosphate pathway (PPP) is the major cellular source of NADPH, an agent critical for oxidative stress defence. The PPP uses glucose, reduces the NADP+ cofactor and produces various sugar phosphates by mutual interconversions. One of the enzymes involved in this latter part is transketolase (TKT). A Leishmania mexicana cell line deleted in transketolase (Δtkt) was assessed regarding viability, sensitivity to a range of drugs, changes in metabolism, and infectivity. The Δtkt cell line had no obvious growth defect in the promastigote stage, but it was more sensitive to an oxidative stress inducing agent and most of the drugs tested. Most importantly, the Δtkt cells were not infective to mice, establishing TKT as a new potential drug target. Metabolomic analyses revealed multiple changes as a consequence of TKT deletion. Levels of the PPP intermediates upstream of TKT increased substantially, and were diverted into additional reactions. The perturbation triggered further changes in metabolism, resembling the ‘stringent metabolic response’ of amastigotes. The Δtkt cells consumed less glucose and glycolytic intermediates were decreased indicating a decrease in flux, and metabolic end products were diminished in production. The decrease in glycolysis was possibly caused by inhibition of fructose-1,6-bisphosphate aldolase by accumulation of the PPP intermediates 6-phosphogluconate and ribose 5-phosphate. The TCA cycle was fuelled by alternative carbon sources, most likely amino acids, instead of glucose. It remains unclear why deletion of TKT is lethal for amastigotes, increased sensitivity to oxidative stress or drop in mannogen levels may contribute, but no definite conclusions can be made. TKT localisation indicated interesting trends too. The WT enzyme is present in the cytosol and glycosomes, whereas a mutant version, truncated by ten amino acids, but retaining a C-terminal targeting sequence, localised solely to glycosomes. Surprisingly, cells expressing purely cytosolic or glycosomal TKT did not have different phenotypes regarding growth, oxidative stress sensitivity or any detected changes in metabolism. Hence, control of the subcellular localisation remains unclear as well as its function. However, these data are in agreement with the presumed semipermeable nature of the glycosome. Further, L. mexicana promastigote cultures were grown in media with different combinations of labelled glucose and ribose and their incorporation into metabolism was followed. Glucose was the preferred carbon source, but when not available, it could be fully replaced with ribose. I also compared metabolic profiles from splenic amastigotes, axenic amastigotes and promastigotes of L. donovani. Metabolomic analysis revealed a substantial drop in amino acids and other indications coherent with a stringent metabolic response in amastigotes. Despite some notable differences, axenic and splenic amastigotes demonstrated fairly similar results both regarding the total metabolic profile and specific metabolites of interest.

This thesis investigates the evolutionary ecology of Homo erectus, focussing on the differential impact of the environment on the species' life history strategy. Departing from previous studies in taking an integrated approach, it examines the related factors of age-specific mortality, encephalisation, and the rate and energetic burden of growth, in order to identify the mechanism by which H. erectus adapted to a diverse range of climates and environments, and how thoroughly that adaptation was achieved. An exploration of the environmental tolerance of H erectus is framed within a model that shows regions that comprised the core of the species, where tolerance is highest and conditions are optimum for growth and reproduction, and periphery regions which fall towards the extremes of tolerance and have repercussive effects on encephalisation, juvenile mortality and growth. Life history traits should vary accordingly, allowing the development of a model for the relationship between environmental variation and the differential evolution of H. erectus. The work is organised thematically. Having provided an overview of evolutionary ecology and introduced the concept of paleo-demes as a means of organising, grouping and understanding the fossils of H. erectus, I address the shortcomings of the r-K dichotomy with a study of age-specific mortality. This work is then applied to patterns of encephalisation, and the energetic implications bf increasing brain size are addressed. A comparative study of two modern human populations supports the prediction that stability of environment translates into stability of growth, and these findings are applied to H. erectus. I demonstrate that H erectus exhibited a long-term trend of an increasing cranial capacity, but that this was not uniform across the species and had varying success, with subsequent energetic stress in the young resulting in high juvenile mortality in some areas. I conclude that the model of core and periphery relates to the latitude of the environment, and that H. erectus was an adaptable and flexible species with a number of strategies available to maximise survival in a range of environmental conditions.

Nature is an invaluable source of inspiration for engineers, who draw upon the solutions evolved by species over millions of years, to design new devices or perfect existing ones. The process of transferring nature's designs into man-made devices is called biomimetics. This thesis reports on a biomimetic study in quantum optics. The microstructure found on the wings of a tropical butterfly holds the secret of its famous structural coloration. The intricate arrangement of low-index dielectric material achieves, in the short wavelength regime of the visible spectrum, an extremely high reflection with a very large angular spread of the back-scattered light and acts as a very effcient low-pass filter. Devices exhibiting these properties may be desirable for applications in a range of elds of optical engineering. An experimental investigation of the scattering of light was performed on the butterfly microstructure. This revealed a more complex phenomenology than previously thought. In order to carry out the measurements, a novel experimental method for the spectroscopical analysis of the scattering from nanostructures surfaces was developed. This method required the construction of an experimental setup involving supercontinuum generation by means of a photonic crystal bre and alignment tools with submicron accuracy. To explain the optical phenomenology of the butter y microstructure, modelling techniques, which are at the forefront of research in the eld of photonic crystals, were used. A theoretical investigation of the band structure of previously unreported crystal lattices occurring in the microstructure was carried out using the plane wave method. A novel numerical method was developed, which enabled computation of the diffraction e ciencies of two-dimensional periodic arrangements of low-index dielectrics. The theoretical investigation accounted correctly for the experimental results. Using common microelectronic processing techniques, two- and three dimensional photonic crystals were fabricated, which were inspired by the butterfly microstructure and which shared some of its optical properties.

The Earth’s climate is changing at an unprecedented rate due to increasing use of fossil fuels and widespread deforestation. This means that the concentration of atmospheric carbon dioxide is increasing, elevating mean global temperatures. In addition, the oceans act as a huge carbon sink and are absorbing more carbon dioxide than they have in the last 650, 000 years causing the oceans to become more acidic. At the beginning of this study the guidelines stated that the control pCO2 concentration for laboratory studies should be 380 µatm (Meehl et al., 2007), concordant with the then current atmospheric pCO2. Four years later, the most recent literature reports that current concentrations of atmospheric pCO2 have now risen to 400 µatm (IPCC, 2013). This demonstrates the unprecedented speed at which our climate is changing and highlights the urgency for research into the potential implications that this change may have on marine systems. In many coastal marine systems calcifying organisms construct biogenic formations that can underpin the ecosystem and form biodiversity hotspots. Calcifying algae and cold water corals are two such organisms. These habitats are economically, politically and socially important. However our knowledge of how these keystone marine organisms may respond in the future is still ambiguous. In general marine calcifiers are likely to be negatively affected, although within some taxa there is considerable variability in their response during climate change studies (e.g. coralline algae and corals). Furthermore, natural variability will overlay the environmental changes associated with anthropogenic global climate change, and as such is likely to significantly influence the response of marine biota to the projected environmental changes. Currently, there are few studies that consider global climate change in the context of natural variability and/ or run long enough to assess acclimatisation potential. Thus, this research aims to provide a better understanding of the impact global climate change may have on key marine calcifiers in the context of natural variability and acclimatisation. This was achieved through a number of laboratory- and field-based studies, utilising well established and adapted techniques. This research focused primarily on red coralline algae. Projected changes in seawater carbonate chemistry mean that marine organisms that utilise dissolved inorganic carbon species as a substrate for multiple physiological processes (i.e. photosynthesis and calcification) are likely to be amongst those most greatly impacted by environmental change. Chapter 3 is the longest laboratory study (24 months), to date, investigating the effects of global climate change on a marine calcifier. Results suggest that seasonal variability in environmental conditions will greatly impact the response of coralline algae to elevated temperature and pCO2. In addition, while calcification may be maintained or increase in response to elevated temperature and/ or pCO2 (chapter 3 and 5) and despite evidence of acclimatisation potential, overall growth was significantly hampered by elevated temperature in the long term. This supports the hypothesis that dissolution may in fact be the primary threat to marine calcifiers, as opposed to impaired calcification. Irradiance is key in coralline algal photosynthesis yet the role of light availability on mediating coralline algal responses to multiple stressors remains scant. The present study examined net photosynthesis and photosynthetic characteristics in the free-living coralline algae, Lithothamnion glaciale in response to sub-diel changes in irradiance in algae exposed to elevated temperature and pCO2 (chapter 4). Observations suggest that light availability will mediate the response of coralline algae to global climate change in the future, as optimal light for photosynthesis increases with increasing temperature and pCO2 (chapter 3, 4 and 5). Cold-water corals make up some of the most heterogeneous, biologically diverse, three-dimensional ecosystems known in the deep sea. However, due to the difficulty in accessing these habitats, to date there is little information about how these organisms may respond to global climate change. The present study provides evidence of intraspecific variability in the response of cold water corals to global climate change that may be dependent upon their prior environmental experience (chapter 7). In situ acclimatisation to variable and low pH may provide cold water corals with the physiological flexibility to acclimatise and adapt to global climate change in the future. Evidence of intraspecific differences in physiology and morphology were also observed in situ in the brown partially calcifying alga, Padina gymnospora between algae located on the reef crest and more environmentally variable reef flat (chapter 6).

The use of distributional models in forestry is investigated, in terms of their capability of modelling distributions of forest mensurational attributes, for modelling and inventory purposes. Emphasis is put on: (i) the univariate and bivariate modelling of tree diameters and heights for stand-level modelling work, and (ii) heuristic methods for use and analysis of distributions which occur in multi-temporal EO imagery, (for the inventory-related tasks of land-use mapping, change detection and growth modelling). In univariate distribution modelling, a new parameterization of the widely-used Johnson’s SB distribution is given, and new Logit-Logistic, generalised Weibull and the Burr system (XII, III, IV) models are introduced into forest modelling. The Logit-Logistic distribution is found to be the best among those compared. The use of regression-based methods of parameter estimation is also investigated. In the domain of bivariate distribution modelling of tree diameters and heights the Plackett method (a particular form of copula) is used to construct Plackett-based bivariate Beta, S­B and Logit-Logistic distributions, (the latter two are new), which are compared with each other and the SBB­ distribution. Other copula functions, including the normal copula, are further employed (for the first time in forest modelling) to construct bivariate distributional models. With the normal copula, the superiority of the Logit-Logistic in the univariate domain is extended into the bivariate domain. To use multi-temporal EO imagery, two pre-processing procedures are necessary: image to image co-registration, and radiometric correction. A spectral correlation-based pixel-matching method is developed to “refine” manually selected control points to achieve very accurate image co-registration. A robust non-parametric method of spectral-distribution standardization is used for relative radiometric correction between images. Finally, possibilities for further research are discussed.

This thesis investigates the systematics and biology of Neotropical Cassidinae and summarizes available knowledge of all tribes occurring in the Neotropics. This study uses a multidisciplinary framework to evaluate various issues in the taxonomy of this diverse group of beetles as a result of extensive field research.

The action of ricin A chain on eukaryotic ribosomes was investigated from a number of different angles. It was shown that ricin A chain modified the rRNA from the 60S subunit of a number of eukaryotic ribosomes, including plant ribosomes, and that the site of action was at the same position in a highly conserved sequence which had previously been identified as the site of action in rat liver 28S rRNA. Investigations into the partial reactions of protein synthesis inhibited in ricin A chain-treated ribosomes showed that both initiation and elongation were inhibited, contradicting the assumption based on previous work that ricin A chain inhibited just the elongation cycle. In a rabbit reticulocyte lysate it was found that whilst elongation was severely inhibited by ricin A chain, the rate of initiation was also reduced approximately six-fold relative to that seen with an inhibitor of just elongation. Furthermore, experiments carried out to investigate the inhibition of elongation showed that this was most likely due to the inhibition of the elongation factor 2 catalysed step. Using an assay which allowed the N-glycosidase activity of ricin A chain to be measured directly it was possible to show that ribosomes from a number of different sources varied markedly in their sensitivity to ricin A chain. Wheat germ ribosomes were shown to be in the order of 1000 times less sensitive to modification than those from either yeast or rabbit reticulocytes. However, this difference does not seem to be a reflection of the differential affinity of ricin A chain for the various substrates but rather a consequence of the ability of the toxin to modify the rRNA once it has bound. This is because kinetic experiments showed that the Km for the reaction on wheat germ ribosomes was similar to that which had been published for the action of ricin A chain on rat liver or rabbit ribosomes. The Kcat, however, was approximately 3 orders of magnitude smaller. A similar picture was seen with the type 1 RIP dianthin 32. It was shown directly that elongation factor 2 bound irreversibly to the ribosome could protect the ribosome from the action of ricin A chain and that in a wheat germ lysate this ability to compete out ricin A chain seemed to be a property of just this supernatant protein. This protection is reflected in the finding that the elongation factor 2 content of purified ribosomes determines their sensitivity to depurination by ricin A chain and that the removal of this protein with high salt sensitises the ribosomes to modification.

Erwinia carotovora subsp. carotovora (Ecc) secretes a variety of extracellular enzymes, namely pectinases (Pel), cellulases (Cel) and proteases (Prt). Some of these extracellular enzymes are considered to be the major pathogenicity determinants of this bacterium. Using the chemical mutagen ethyl methyl sulphonate (EMS), a range of Ecc mutants defective in extracellular enzyme production have been generated. One class was found to be pleiotropically defective in the production of Pel and Cel but unaffected for Prt production. Pel and Cel were still synthesised in this class of mutant but both enzymes accumulated within the periplasm. Mutants of the Pel-, Cel-, Prt+ class have been termed Out- mutants. A single Out- mutant, RJP190, was partially resistant to infection by two Ecc bacteriophages. Using a cosmid library of wild-type Ecc, 12 of the 14 Out- mutants were complemented to Out+. Further analysis of the complementing cosmids led to the identification of at least six out loci. A 3.7 kb region of DNA containing out genes was sequenced. This fragment of DNA overlapped with other out genes sequenced In this laboratory. The contiguous DNA (5.7 kb) encoded four proteins, OutD, OutE, OutF and OutG, which were visualised using a T7 directed expression system. The predicted Out proteins were found to share homology with other eubacterial proteins involved in macromolecular trafficking. Accumulated findings strongly suggest that this Out-type system is the major pathway used by Gram-negative bacteria for secreting proteins to the extracellular milieu.

The wildlife trade represents a significant threat to biodiversity, but may also provide opportunities for societal and economic benefits. To supply the trade, wildlife is often sourced from biodiverse developing countries where poverty rates are high. Ensuring a legal and sustainable trade is therefore critical not only for conservation and implementation of the Convention on International Trade in Endangered Species (CITES), but can contribute to UN Sustainable Development Goals to reduce poverty in developing regions. This thesis investigates trade in live animals, with emphasis on socio-economic implications of wildlife trade chains, and how these interact with conservation and sustainable use in supply countries. An interdisciplinary approach utilises global analysis of wildlife trade data; social research methods to examine the trade in Madagascar; and a specialised questioning technique to explore sustainability of the trade at the end-user level. The findings demonstrate an increasing component of the reptile pet trade comprises animals from ranching operations, or captive-bred in consumer countries. Although this may take pressure off wild populations, it may have implications for biodiversity and benefit sharing in supply countries. In Madagascar, a small proportion of the export value of reptiles and amphibians reaches local collectors. Whilst being potentially profitable and providing additional cash income to some households, wildlife trapping is also unreliable, part-time and financially risky. Consequently, it appears to bring limited opportunities for poverty alleviation or incentives for conservation at the local scale. Value chain analysis reveals the informal and complex nature of the supply chain, making design and implementation of interventions to enhance the trade challenging. Findings suggest that initiatives may be most effective working at the local level to improve organisation and cooperative management of the trade. At the consumer end, mortality of pet reptiles varies between taxa but appears to be relatively low. This directly informs debate concerning exotic pet keeping in consumer countries, for which there are limited data concerning sustainability of wildlife supply chains. Together, these studies enhance knowledge regarding implications of the wildlife trade for livelihoods and conservation, and inform dialogue concerning wildlife trade policy and practice more generally.